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Sixteen new SARS-CoV-2 lineages spread through South Africa from March to August 2020

An analysis of more than 1,300 near-whole genome sequences of SARS-CoV-2 isolated in South Africa during the first 6 months of the pandemic revealed 16 new lineages of the virus. These findings shed light on the spread of SARS-CoV-2 throughout South Africa from 6 March to 26 August 2020.

The COVID-19 pandemic in South Africa is the largest in Africa, with more than 785,000 people infected (which accounted for approximately 50% of all known African infections) and more than 20,000 deaths by the end of November 2020.

Genomic epidemiology has been used to understand the evolution of SARS-CoV-2 and to track the dynamics of transmission across the world. Houriiyah Tegally, Tulio de Oliveira and colleagues at the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal analysed 1,365 near-whole genomes of SARS-CoV-2 collected in South Africa during the first 6 months of the pandemic and identified 16 new lineages. Most of these lineages have unique mutations that have not been identified elsewhere. The authors found that three of these lineages – B.1.1.54, B.1.1.56 and C.1 – spread widely in South Africa during the first wave, accounting for around 42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, was the most geographically widespread lineage in South Africa by the end of August 2020.

The authors conclude that this type of genomic surveillance can be used on a large scale in Africa to identify new lineages of SARS-CoV-2 and to inform measures to control the spread of the virus. Such genomic surveillance was crucial in the identification of the 501Y.V2 variant in South Africa in December 2020.

Study details

Sixteen novel lineages of SARS-CoV-2 in South Africa

Houriiyah Tegally, Eduan Wilkinson, Richard J. Lessells, Jennifer Giandhari, Sureshnee Pillay, Nokukhanya Msomi, Koleka Mlisana, Jinal N. Bhiman,Anne von Gottberg, Sibongile Walaza, Vagner Fonseca, Mushal Allam, Arshad Ismail, Allison J. Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Carolyn Williamson, Francesco Petruccione, Alex Sigal, Inbal Gazy, Diana Hardie, Nei-yuan Hsiao, Darren Martin, Denis York, Dominique Goedhals, Emmanuel James San, Marta Giovanetti, José Lourenço, Luiz Carlos Junior Alcantara, Tulio de Oliveira

Published in Nature Communications on 2 February 2021

Abstract
The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020.

 

[link url="https://www.nature.com/articles/s41591-021-01255-3"]Nature Communications study (Restricted access)[/link]

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